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- PDB-5adk: Structure of bovine endothelial nitric oxide synthase heme domain... -

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Basic information

Entry
Database: PDB / ID: 5adk
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 7-((3-(Dimethylamino)methyl)phenoxy)methyl)quinolin-2- amine
ComponentsNITRIC OXIDE SYNTHASE, ENDOTHELIAL
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure ...cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / mitochondrion organization / caveola / blood coagulation / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to lipopolysaccharide / cytoskeleton / calmodulin binding / heme binding / Golgi apparatus / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily ...Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-7M3 / ACETATE ION / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 3
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Phenyl Ether- and Aniline-Containing 2-Aminoquinolines as Potent and Selective Inhibitors of Neuronal Nitric Oxide Synthase.
Authors: Cinelli, M.A. / Li, H. / Pensa, A.V. / Kang, S. / Roman, L.J. / Martasek, P. / Poulos, T.L. / Silverman, R.B.
History
DepositionAug 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE, ENDOTHELIAL
B: NITRIC OXIDE SYNTHASE, ENDOTHELIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,27015
Polymers99,4542
Non-polymers2,81613
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-120.4 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.962, 106.382, 157.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRIC OXIDE SYNTHASE, ENDOTHELIAL / CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / ENDOTHELIAL ...CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / ENDOTHELIAL NITRIC OXIDE SYNTHASE


Mass: 49727.012 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, UNP RESIDUES 40-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 7 types, 515 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#4: Chemical ChemComp-7M3 / 7-[[3-[(dimethylamino)methyl]phenoxy]methyl]quinolin-2-amine


Mass: 307.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N3O
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUE 100 IS FOUND AS AN ARG IN STRUCTURE BUT IS A CYS IN DATABASE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.8 %
Description: OVERALL RMERGE 0.082 RPIM0.056 CC ONE HALF 0.999 HIGHEST RESOLUTION SHELL RMERGE 3.157 RPIM 2.226 CC ONE HALF 0.260
Crystal growpH: 6
Details: 20-22% PEG3350 0.1M CACODYLATE, 140-200 MM MG ACETATE 5 MM TCEP, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 89217 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 32.45 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.5 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.805→39.19 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 20.82 / Stereochemistry target values: ML
Details: RESIDUES 110 TO 120 IN CHAIN A AND 111 TO 120 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.1934 4369 5 %
Rwork0.164 --
obs0.1655 88058 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.805→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6526 0 195 502 7223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076924
X-RAY DIFFRACTIONf_angle_d1.1989457
X-RAY DIFFRACTIONf_dihedral_angle_d16.062496
X-RAY DIFFRACTIONf_chiral_restr0.073984
X-RAY DIFFRACTIONf_plane_restr0.0051217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8054-1.82590.3493960.3141906X-RAY DIFFRACTION69
1.8259-1.84740.35291180.31762554X-RAY DIFFRACTION91
1.8474-1.86990.3841580.29832827X-RAY DIFFRACTION99
1.8699-1.89360.30381400.29442759X-RAY DIFFRACTION99
1.8936-1.91850.3231530.28022792X-RAY DIFFRACTION99
1.9185-1.94480.29021360.27382790X-RAY DIFFRACTION99
1.9448-1.97250.271470.24722799X-RAY DIFFRACTION100
1.9725-2.0020.28281410.23712842X-RAY DIFFRACTION100
2.002-2.03330.27171590.2282761X-RAY DIFFRACTION100
2.0333-2.06660.26591470.22772862X-RAY DIFFRACTION100
2.0666-2.10220.27191390.19722778X-RAY DIFFRACTION100
2.1022-2.14050.22781590.19322815X-RAY DIFFRACTION99
2.1405-2.18160.23321440.18982764X-RAY DIFFRACTION98
2.1816-2.22620.20491480.17472821X-RAY DIFFRACTION99
2.2262-2.27460.20921360.17442806X-RAY DIFFRACTION99
2.2746-2.32750.20891480.16822824X-RAY DIFFRACTION100
2.3275-2.38570.18661530.16782812X-RAY DIFFRACTION99
2.3857-2.45010.23071460.16692815X-RAY DIFFRACTION100
2.4501-2.52220.20781670.16662835X-RAY DIFFRACTION100
2.5222-2.60360.20211620.15652804X-RAY DIFFRACTION100
2.6036-2.69670.18831450.16042827X-RAY DIFFRACTION99
2.6967-2.80460.22511390.16562801X-RAY DIFFRACTION98
2.8046-2.93220.20761240.16252874X-RAY DIFFRACTION100
2.9322-3.08670.1961600.15772843X-RAY DIFFRACTION100
3.0867-3.280.19471430.15722866X-RAY DIFFRACTION100
3.28-3.53320.17211520.14262864X-RAY DIFFRACTION99
3.5332-3.88840.15691570.13252867X-RAY DIFFRACTION99
3.8884-4.45040.14611460.12812844X-RAY DIFFRACTION97
4.4504-5.60440.16631350.13752939X-RAY DIFFRACTION100
5.6044-39.19930.15381710.16252998X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8205-0.2468-0.4421.31690.15881.2808-0.0064-0.01330.0128-0.09690.0448-0.1662-0.02130.0827-0.03740.2024-0.02120.00590.1952-0.00680.224111.833310.310532.0595
20.8745-0.29290.28171.0844-0.94852.43760.0324-0.115-0.05230.05910.04990.0040.0148-0.1124-0.07480.1989-0.0002-0.0040.2054-0.00630.21272.58475.925967.95
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 67:482)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 69:482)

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